Can a monster that takes a class, lets say a doppelganger that takes a level of rogue take an archetype as well?
Hero lab doesn't seem to want to let me do that.
(This might be more fitting for the advice section)
According to the rules... yes... kinda.
The are not always balanced in terms abilities that a player character should have, but non-player race creatures are allowed to take class levels. This is probably why hero lab doesn't do it. I'm not a rep from them or anything though so take what I say with a pinch of salt.
If you are looking at doing a player character as one, it might be a smart idea to built it with the Racial Guide.